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Using BioSlax and the BioSlax Server

BioSlax is a comprehensive live CD based on Slackware Linux, tailored specifically for bioinformatics applications. Developed by the Bioinformatics Centre at the National University of Singapore, BioSlax operates independently from existing operating systems, providing a modular environment for users to add or remove bioinformatics tools effortlessly. With its unique Unification File System, BioSlax enhances flexibility and ease of use, making it ideal for genome analysis. This course from the HKU-Pasteur Research Centre will guide participants in using BioSlax effectively from August 17 to August 29, 2009.

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Using BioSlax and the BioSlax Server

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  1. Using BioSlax and the BioSlax Server Tin Wee Tan National University of Singapore Bioinformatic and Comparative Genome Analysis Course HKU-Pasteur Research Centre - Hong Kong, China August 17 - August 29, 2009

  2. What is BioSlax? • Slackware Linux on a CD + bioinformatics modules included • Released by Bioinformatics Centre (BIC), NUS • Uses Unification File System (aufs) that allows read-only file system to have writable access by saving all changes in memory • Slax - created by Tomas Matejicek. Website is at: http://www.slax.org/

  3. Why use BioSlax/Slax? • Complete OS by itself running off a CD • Uses computer’s memory to load itself • Isolated from and independent of OS already installed on hard disk (eg. Windows XP, Windows Vista, etc) • Need not format hard disk for installation. Existing data stays intact • Modular

  4. Modularity of BioSlax • There are 2 parts to the BioSlax build • Part 1: core system (Linux OS + basic tools) • Part 2: modules • Modules • individual utilities user wants • easily added or removed prior to CD creation • easily upgraded when new version’s available

  5. Modules in BioSlax … • Bioinformatics Modules:

  6. Booting Up Bioslax • CD (without Open Office) • DVD (with Open Office) • USB drive (with Open Office)

  7. Configuring your Boot Device Priority of the BIOS of your PC • When you boot up your computer. Press F2 (or F1/ESC/DELETE etc) to enter the BIOS Configuration mode (Setup) • Select the BOOT tab, and the BOOT device priority list • Select CD-Rom to be the first boot device by using the arrow/F5/Pg Up key. If you are booting from USB drive – Select “USB Key” to be the second boot device • Save and Exit

  8. Screenshot – Bioslax Booting Up

  9. Screenshot – Bioslax Booting Up

  10. Running Bioslax on Windows Using VMware player • Download and install VMware Player • http://www.vmware.com/download/player/ • Download BioSlax Version Customized For VMPlayer • Unzip to C drive (e.g. C:\BS71VMCD) • Run VMPlayer and open C:\ BS71VMCD \Other Linux 2.6.x kernel.vmx

  11. Setting up your internet connection in VMware version of Bioslax • Change the network setting (on the top menu) from “Bridged” to “NAT” • Open Konsole • Type “dhcpcd” and press “Enter”

  12. Screenshot – VMWare Version

  13. The X-Window Desktop

  14. How to create a Slax module • To convert tgz package to Slax module: • tgz2lzm <application.tgz> <application.lzm> • e.g.tgz2lzm blast.tgz blast.lzm • To install an application to a separate directory: • dir2lzm <directory> module.lzm • e.g. dir2lzm /usr/local/blast blast.lzm

  15. How to use a Slax module • To create own LiveCD: • save modules in /modules directory of the CD • To activate a module, use: • activate </path/module.lzm> • e.g. activate /tmp/blast.lzm • To deactivate a module, use: • deactivate </path/module.lzm> • e.g. deactivate /tmp/blast.lzm

  16. How to save/restore settings • To save and restore your settings, hit the ‘TAB’ key at the BioSLAX boot menu selection. Use: • changes=/mnt/sda1_removable/mychanges • where /mnt/sda1_removable is a mounted USB drive • and /.../mychanges is a directory created in the USB drive to store settings

  17. Network setup • Open Konsole and type iwconfig to list all possible wireless devices on the system • Wireless Asst  Select your wireless device (can be referred to as wlanX, wifiX, athX, brX, ethX) • If you don't have a built in wireless device, plug in your external wireless card before running Wireless Asst. • Select DHCP and a pop up message will appear at the bottom right if the card successfully obtains an IP address. Run Mozilla, the web browser

  18. Web BLAST demo • Insert your USB drive into the PC • Make sure your USB drive is detected

  19. Web BLAST demo • If you don’t see the db directory, open Konsole & type: • cd /mnt/sda1_removable/ • wgetftp://sf01.bic.nus.edu.sg/incoming/blast-db-demo.tar.gz • tar –zxf blast-db-demo.tar.gz

  20. Web BLAST demo • To setup BLAST database, go to K-Menu -> BioSLAX -> Desktop Apps -> BLAST DB Setup • Fill in the location of the BLAST formatted database files

  21. Web BLAST demo • Start web BLAST & select the list of BLAST programs:

  22. Web BLAST demo • Regular BLAST page

  23. Web BLAST demo • BLAST result

  24. Recommended reading • http://www.slax.org/ • http://www.bioslax.com/ • http://www.slax.org/documentation.php

  25. Hands-On Practice • htdocs and cgi-bin folders • Modules

  26. Bioslax as server • Host BLAST database • 2. Hosting web server

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